There are some forces that can never coexist peacefully, that, when they meet, must play a zero sum game for power in which one will always be dominant. The McFlys and the Tannens are such forces, drawn together again and again throughout history only so one can exert control over the other. The Tannens were always more powerful and would have stayed so if a McFly hadn’t befriended Doc Brown who was able to retroactively aid the McFly clan. Not only that, he went to the future to make sure that the McFlys had the upper hand in all future generations.
Travelling across time and space in his flying train, Doc Brown aided the future generations of McFlys against the Tannens as their numbers grew. Eventually, most of the world’s population was either a Tannen or McFly descendant, and those who weren’t had to pick sides. There’s no way to tell how many times the final battle was fought, Doc Brown effectively rewriting any time stream in which the McFlys lost. But eventually the brutish Tannens were vanquished and forced underground while the spritely McFlys and their allies enjoyed life on the surface during a technological golden age. Satisfied that all was well with the world, Doc Brown flew off into the sunset.
Time passed, hundreds of thousands of years of natural selection changed the two societies so that those on the surface and those beneath barely resembled the men they once were let alone each other. Eventually another time traveler arrived, in the year 802,701 A.D. This time traveler had never heard of the McFlys and the Tannens or their war for supremacy; the traveler only saw the distant echoes of what they once were. So he came up with his own names to describe the descendants: Eloi and Morlocks.